GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AO353_03040 in Echinicola vietnamensis KMM 6221, DSM 17526

Align ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized)
to candidate Echvi_2204 Echvi_2204 ABC-type antimicrobial peptide transport system, ATPase component

Query= reanno::pseudo3_N2E3:AO353_03040
         (254 letters)



>FitnessBrowser__Cola:Echvi_2204
          Length = 240

 Score =  137 bits (346), Expect = 2e-37
 Identities = 87/244 (35%), Positives = 138/244 (56%), Gaps = 18/244 (7%)

Query: 4   LEVQDLHKRY--GSHEV--LKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGK 59
           +E +++ K Y  G+ +V  LK V++    G+ ++ +G SGSGKST +  I  L+ P AG 
Sbjct: 5   IETKEIKKTYVMGAEKVQALKSVTIDIIKGEYVAFMGPSGSGKSTLMNIIGCLDTPTAGN 64

Query: 60  ILLNNEELKLVANKDGALKAADPKQLQRMRSR-LSMVFQHFNLWSHMTAMENIMEAPVHV 118
            +LNN+++  +   +          L  +R++ +  VFQ FNL    T +EN+   P+  
Sbjct: 65  YILNNKDVSHMTENE----------LAEIRNKEIGFVFQTFNLLPRATCLENVA-LPLIY 113

Query: 119 LGMSKAEAREKAELYLAKVGVSHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTS 178
            G SK++  +KA L L  VG+  R    P  +SGG++QRVAIARAL  +P ++L DEPT 
Sbjct: 114 AGYSKSDREDKAFLALKSVGLEDRIHHKPNELSGGQRQRVAIARALVNDPSIILADEPTG 173

Query: 179 ALDPELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVE-ESGNPREVL 237
            LD +   D++ +   L Q+G T+++VTHE   A   ++++V L  G+VE +  NP    
Sbjct: 174 NLDTKTSYDIMNLFDELHQKGNTIIMVTHEDDIA-HYAHRIVRLRDGLVETDQNNPNPTR 232

Query: 238 VNPQ 241
            N Q
Sbjct: 233 NNFQ 236


Lambda     K      H
   0.317    0.131    0.364 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 138
Number of extensions: 6
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 254
Length of database: 240
Length adjustment: 24
Effective length of query: 230
Effective length of database: 216
Effective search space:    49680
Effective search space used:    49680
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory